This is from your recon-all.log
"
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz
mri_convert: extra argument
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
"
There is a space in your path to nii.gz. Can you remove the space by renaming
the directory?
Also, your SUBJECTS_DIR points to your Freesurfer install directory -
/usr/local/freesurfer/subjects. You might run into permission or symbolic link
problems later. It is a good idea to set SUBJECTS_DIR to some other directory
where you have write permissions.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
External Email - Use Caution
Hi FreeSurfer Team,
I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \
-all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all
failed before completeing even the first step. I tried other files from our
dataset and using .nii files and got the same result. I saw a recent thread
<https://secure-web.cisco.com/1dNYuQ5feZYQ6hNc76goinSvD-Ypnc3onN5YQA8IZaGD9ZMsgPU8h02eq6smQW_JlVSoe2pmWi9i4IcVcvgPNAErLGWflT-2DHnEGZhHuYuSO7uagH4fed_iEleZMZ8fgVidAMFlNu_V6xq1SiHRk7nBL5_vNP6s-l8W5JP5TtFTlM7qsiZb0cfyjC0beae7q8RstHZ1a7H1bThMO8tUOdBPq6h2mtRu15a6hLnBK4v7YbPIeyWQj1PNy1poAzCsu_PpjvCs0OTiVKjJIHv6obmHjItvr-tP8RedoW0g4wzOQSCgST1rQnUsemz7IcLPP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg62253.html>
where someone's issue was improperly labeled WM lesions but my dataset is
composed of healthy brains.
I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer
version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me
know if you have any questions!
Thanks,
Abeoseh Flemister
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